As one of the important water sources of the desert ecosystem in the Tarim Basin, the largest fishery base in Xinjiang, and the former largest inland and freshwater lake of China, the water quality of Bosten Lake is worthy of government and public attention. To determine the water’s hydrochemical composition and the water quality of Bosten Lake, analyses of the spatial distribution, water pollution status and irrigation suitability were conducted with statistical methods, including redundancy and factor analyses, inverse distance weighted interpolation, and water quality assessment and saturation index simulation of minerals in the water from a survey done in 2018. The results suggested that the average total dissolved solids (TDS) of Bosten Lake in 2018 was 1.32 g/L, and the lake is alkaline with a pH of 8.47. The strength of the water exchange capacity affected the spatial distribution of TDS. The spatial distribution of TDS and its value can be significantly changed by restoring the water supply of seasonal rivers in the northwest. The water of Bosten Lake contains sulfate and sodium groups, which are mainly affected by lake evaporation. As the pH increases, the content of carbonate ions increases, while the content of bicarbonate ions decreases. The spatial distributions of other major ions are consistent with that of the TDS. The spatial distribution of potentially toxic elements is more complicated than that of major ions. In general, the spatial distribution of Cu and As is more consistent with the spatial distribution of electrical conductivity or TDS. The spatial distributions of the Zn, Se and pH values are more consistent with respect to other variables. Although the water of Bosten Lake is still at a permissible level for water irrigation, the lake is moderately polluted, and the local site almost has a highly polluted status. The research results are of great significance for lake environmental protection and management as well as watershed ecological restoration.